rs10088485

chr8-17389053-G-Achr8-17389053-G-Cchr8-17389053-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004686.5(MTMR7):c.25-15813C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,726 control chromosomes in the GnomAD database, including 12,825 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.40 (12825 hom., cov: 32)
• Consequence: MTMR7 NM_004686.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.74

Genes affected

MTMR7 (HGNC:7454): (myotubularin related protein 7) This gene encodes a member of the myotubularin family of tyrosine/dual-specificity phosphatases. The encoded protein is characterized by four distinct domains that are conserved among all members of the myotubularin family: the glucosyltransferase, Rab-like GTPase activator and myotubularins domain, the Rac-induced recruitment domain, the protein tyrosine phosphatases and dual-specificity phosphatases domain and the suppressor of variegation 3-9, enhancer-of-zeste, and trithorax interaction domain. This protein dephosphorylates the target substrates phosphatidylinositol 3-phosphate and inositol 1,3-bisphosphate. A pseudogene of this gene is found on chromosome 5. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.548 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MTMR7	NM_004686.5	c.25-15813C>T		intron_variant		ENST00000180173.10
MTMR7	XM_047422407.1	c.-324-15813C>T		intron_variant
MTMR7	XM_047422408.1	c.25-15813C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MTMR7	ENST00000180173.10	c.25-15813C>T		intron_variant		1	NM_004686.5	P1
MTMR7	ENST00000521857.5	c.25-15813C>T		intron_variant		5
MTMR7	ENST00000517317.5	c.25-15813C>T		intron_variant, NMD_transcript_variant		5
MTMR7	ENST00000521177.1	n.261-15813C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60607 AN: 151604 Hom.: 12815 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.503

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.400 AC: 60643 AN: 151726 Hom.: 12825 Cov.: 32 AF XY: 0.403 AC XY: 29840 AN XY: 74112

Gnomad4 AFR AF: 0.280

Gnomad4 AMR AF: 0.558

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.439

Alfa AF: 0.348 Hom.: 1712

Bravo AF: 0.408

Asia WGS AF: 0.360 AC: 1251 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.0020
Dann	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10088485; hg19: chr8-17246562;